bob_week4 > ./hand-in2.pl dengue_virus_4.gb 
Nucleotide occurences:
A: 3298 (31.0 %)
G: 2804 (26.3 %)
T: 2333 (21.9 %)
C: 2214 (20.8 %)

All DNA words of length 2:
GA: 990
AG: 911
CA: 883
TG: 841
AA: 783
AT: 681
AC: 673
GG: 673
CT: 542
GT: 515
TC: 505
GC: 471
TT: 466
CC: 455
TA: 391
CG: 224

Will perform permutations test to estimate backgroud distribution:
How many permutations? 5000
Completed 5000 out of 5000 permutations
GA: 990 NOT within [782, 954] (mean = 868)
AG: 911     within [783, 953] (mean = 868)
CA: 883 NOT within [607, 763] (mean = 685)
TG: 841 NOT within [538, 689] (mean = 614)
AA: 783     within [717, 841] (mean = 779)
AT: 681     within [643, 802] (mean = 723)
AC: 673     within [608, 763] (mean = 685)
GG: 673 NOT within [525, 643] (mean = 584)
CT: 542     within [415, 554] (mean = 484)
GT: 515 NOT within [538, 690] (mean = 614)
TC: 505     within [415, 554] (mean = 484)
GC: 471 NOT within [508, 657] (mean = 583)
TT: 466     within [364, 473] (mean = 418)
CC: 455 NOT within [328, 433] (mean = 380)
TA: 391 NOT within [643, 803] (mean = 723)
CG: 224 NOT within [508, 658] (mean = 583)